package biocaml

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The OCaml Bioinformatics Library

Install 

dune-project
 Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

  1. S
    Sebastien Mondet
  2. A
    Ashish Agarwal
  3. P
    Philippe Veber
  4. C
    Christophe Troestler
  5. S
    Sergei Lebedev
  6. D
    David Koppstein
  7. A
    Alexander Gryzlov
  8. F
    Francois Berenger

Maintainers

  1. B
    biocaml@googlegroups.com

Sources

v0.10.0.tar.gz
md5=497e3f2f7128a6ca347d66848da38a3d
sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

doc/biocaml.unix/Biocaml_unix/Histogram/index.html

Module Biocaml_unix.Histogram

Histograms with polymorphic bin types.

A histogram is a list of bins, each with a count. Bin i is defined by a lower limit lo(i) and an upper limit hi(i). It is inclusive of the lower limit and exclusive of the upper limit. For all i, hi(i) = lo(i+1). By convention the first bin is numbered 0. The count of a bin is a floating point number, allowing fractional values if necessary.

type 'a t

The type of a histogram whose bin limits are of type 'a.

val make : ('a -> 'a -> int) -> 'a list -> 'a t option

make cmp bins returns a new histogram from the given bins, all initialized to a count of 0.0. The bins must be provided as a list of the boundaries dividing them. The list [v0; v1; ...; vn] of length n+1 represents the n bins [v0, v1), [v1, v2), ..., [vn-1, vn), where cmp is used as the comparison function. Returns None if bins are not monotonically increasing, or if length of bins is less than 2.

val to_list : 'a t -> (('a * 'a) * float) list

Return a list of all bin/count pairs. Answer will be in ascending order by the bin limits.

val copy : 'a t -> 'a t

Copy histogram.

val bin : 'a t -> int -> ('a * 'a) option

bin hist i returns the ith bin of hist.

val bin_exn : 'a t -> int -> 'a * 'a

bin hist i returns the ith bin of hist. Raise Invalid_argument if an invalid bin number is requested.

val count : 'a t -> int -> float option

count hist i returns the count the ith bin.

val count_exn : 'a t -> int -> float

count hist i returns the count the ith bin. Raise Invalid_argument if an invalid bin number is requested.

val num_bins : 'a t -> int

Number of bins.

val minimum : 'a t -> 'a

Lower limit of the minimum bin.

val maximum : 'a t -> 'a

Upper limit of the maximum bin.

val increment : ?delt:float -> 'a t -> 'a -> 'a t

increment delt hist x increments the count of the bin containing x by delt (default is 1.0). The histogram is unaltered if x not in any bin. This is not considered an error because it is often necessary to calculate a histogram for a subset of a larger data set.

val reset : 'a t -> 'a t

Return histogram with same bins but all counts reset to 0.0.

val find_bin_index : 'a t -> 'a -> int option

find_bin_index hist x returns the index of the bin in hist containing x. Return None if x is outside the histogram's range.

val in_range : 'a t -> 'a -> bool

in_range hist x is true if x greater than or equal to minimum hist and strictly less than maximum hist.

Histograms With Float Bins
val make_uniform : float -> float -> int -> (float t, string) Core_kernel.Result.t

make_uniform min max n returns a histogram with n bins uniformly dividing up the range from min to max. Bins will be inclusive of the lower limit and exclusive of the upper limit, i.e. value of min will fall into lowest bin and value of max will fall outside the range of the histogram. Raise Failure if min not strictly less than max or if n not greater than 0.